Unverified Commit f26e90f7 authored by mvdbeek's avatar mvdbeek
Browse files

Log start and end of request 

Configurable via `use_access_logging_middleware`.
Looks like this:

```
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:43,776 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:48,719 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,767 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,786 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4 200
galaxy.webapps.base.api DEBUG 2024-04-23 17:14:53,139 [pN:main,p:73562,tN:MainThread] GET /api/entry_points?running=true 763693e9-4fd3-4a97-a100-a3c259b4b4c8
```
parent 8f4968f0

doc/source/admin/galaxy_options.rst

+11 −3
Original line number Diff line number Diff line
@@ -3030,6 +3030,17 @@ 
:Type: bool





~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``use_access_logging_middleware``

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



:Description:

    Log request start as well as request end. Disables uvicorn access

    log handler.

:Default: ``false``

:Type: bool





~~~~~~~~~~~~

``use_lint``

~~~~~~~~~~~~
@@ -5477,6 +5488,3 @@ 
    This requires the help_forum_api_url to be set.

:Default: ``false``

:Type: bool

lib/galaxy/config/sample/galaxy.yml.sample

+4 −0
Original line number Diff line number Diff line
@@ -1743,6 +1743,10 @@ galaxy: 
  # job is complete.

  #debug: false



  # Log request start as well as request end. Disables uvicorn access

  # log handler.

  #use_access_logging_middleware: false



  # Check for WSGI compliance.

  #use_lint: false

lib/galaxy/config/schemas/config_schema.yml

+7 −0
Original line number Diff line number Diff line
@@ -2193,6 +2193,13 @@ mapping: 
          causes the files used by PBS/SGE (submission script, output, and error)

          to remain on disk after the job is complete.



      use_access_logging_middleware:

        type: bool

        default: false

        required: false

        desc: |

          Log request start as well as request end. Disables uvicorn access log handler.



      use_lint:

        type: bool

        default: false

lib/galaxy/webapps/base/api.py

+35 −1
Original line number Diff line number Diff line 
import os

import stat

import typing

import uuid

from logging import getLogger



import anyio

from fastapi import (
@@ -15,8 +17,12 @@ from starlette.responses import ( 
    FileResponse,

    Response,

)

from starlette_context import context

from starlette_context.middleware import RawContextMiddleware

from starlette_context.plugins import RequestIdPlugin

from starlette_context.plugins import (

    Plugin,

    RequestIdPlugin,

)



from galaxy.exceptions import MessageException

from galaxy.exceptions.utils import api_error_to_dict
@@ -32,6 +38,9 @@ if typing.TYPE_CHECKING: 
    )





log = getLogger(__name__)





# Copied from https://github.com/tiangolo/fastapi/issues/1240#issuecomment-1055396884

def _get_range_header(range_header: str, file_size: int) -> typing.Tuple[int, int]:

    def _invalid_range():
@@ -192,6 +201,31 @@ def add_exception_handler(app: FastAPI) -> None: 
        return get_error_response_for_request(request, exc)





class AccessLoggingMiddleware(Plugin):



    key = "access_line"



    async def process_request(self, request):

        scope = request.scope

        path = scope["root_path"] + scope["path"]

        if scope["query_string"]:

            path = f"{path}?{scope['query_string'].decode('ascii')}"

        access_line = f"{scope['method']} {path} {uuid.uuid4()}"

        log.debug(access_line)

        return access_line



    async def enrich_response(self, response) -> None:

        access_line = context.get("access_line")

        if status := response.get("status"):

            log.debug(f"{access_line} {status}")





def add_raw_context_middlewares(app: FastAPI):

    getLogger("uvicorn.access").handlers = []

    plugins = (RequestIdPlugin(force_new_uuid=True), AccessLoggingMiddleware())

    app.add_middleware(RawContextMiddleware, plugins=plugins)





def add_request_id_middleware(app: FastAPI):

    app.add_middleware(RawContextMiddleware, plugins=(RequestIdPlugin(force_new_uuid=True),))

lib/galaxy/webapps/galaxy/fast_app.py

+5 −1
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ from galaxy.schema.invocation import CustomJsonSchema 
from galaxy.version import VERSION

from galaxy.webapps.base.api import (

    add_exception_handler,

    add_raw_context_middlewares,

    add_request_id_middleware,

    GalaxyFileResponse,

    include_all_package_routers,
@@ -179,6 +180,9 @@ def initialize_fast_app(gx_wsgi_webapp, gx_app): 
    app = get_fastapi_instance(root_path=root_path)

    add_exception_handler(app)

    add_galaxy_middleware(app, gx_app)

    if gx_app.config.use_access_logging_middleware:

        add_raw_context_middlewares(app)

    else:

        add_request_id_middleware(app)

    include_all_package_routers(app, "galaxy.webapps.galaxy.api")

    include_legacy_openapi(app, gx_app)